Identification of Essential Proteins Using Induced Stars in Protein–Protein Interaction Networks
Published Online:14 Jun 2019https://doi.org/10.1287/ijoc.2018.0872
References
- (2009) Towards the prediction of essential genes by integration of network topology, cellular localization and biological process information. BMC Bioinform. 10(1):290.Crossref, Google Scholar
- (2010) Revisiting date and party hubs: Novel approaches to role assignment in protein interaction networks. PLoS Comput. Biol. 6(6):e1000817.Crossref, Google Scholar
- (2006) Identifying sets of key players in a social network. Comput. Math. Organ. Theory 12(1):21–34.Crossref, Google Scholar
- . (2013) The BioGRID interaction database: 2013 update. Nucleic Acids Res. 41(D1):D816–D823.Crossref, Google Scholar
- (2008) A unified scoring scheme for detecting essential proteins in protein interaction networks. 20th IEEE Internat. Conf. Tools Artificial Intelligence, vol. 2 (IEEE, Piscataway, NJ), 66–73.Crossref, Google Scholar
- (2005) Genome-wide screening for gene function using RNAi in mammalian cells. Immunology Cell Biol. 83(3):217–223.Crossref, Google Scholar
- (2006a) Protein bipartivity and essentiality in the yeast protein-protein interaction network. J. Proteome Res. 5(9):2177–2184.Crossref, Google Scholar
- (2006b) Virtual identification of essential proteins within the protein interaction network of yeast. Proteomics 6(1):35–40.Crossref, Google Scholar
- (1999) The centrality of groups and classes. J. Math. Sociol. 23(3):181–201.Crossref, Google Scholar
- (2005) Extending centrality. Models Methods Soc. Network Anal. 35(1):57–76.Crossref, Google Scholar
- (2010) Induced, endogenous and exogenous centrality. Soc. Network 32(4):339–344.Crossref, Google Scholar
- . (2013) String v9. 1: Protein-protein interaction networks, with increased coverage and integration. Nucleic Acids Res. 41(D1):D808–D815.Crossref, Google Scholar
- Gurobi Optimization I (2015) Gurobi optimizer reference manual (Gurobi Optimization, Beaverton, OR). Accessed January 15, 2016, http://www.gurobi.com.Google Scholar
- (2008) Topological properties of protein interaction networks from a structural perspective. Biochemical Soc. Trans. 36(6):1398–1403.Crossref, Google Scholar
- (2008) Exploring network structure, dynamics, and function using NetworkX. Proc. 7th Python Sci. Conf. (SciPy2008), Pasadena, CA.Google Scholar
- (2005) Comparative genomics of centrality and essentiality in three eukaryotic protein-interaction networks. Molecular Biol. Evolution 22(4):803–806.Crossref, Google Scholar
- . (2004) Evidence for dynamically organized modularity in the yeast protein–protein interaction network. Nature 430(6995):88–93.Crossref, Google Scholar
- (2006) How complete are current yeast and human protein-interaction networks? Genome Biol. 7(11):120.Crossref, Google Scholar
- (2006) Why do hubs tend to be essential in protein networks? PLoS Genetics 2(6):e88.Crossref, Google Scholar
- (2001) Lethality and centrality in protein networks. Nature 411(6833):41–42.Crossref, Google Scholar
- (2015) Essential protein identification based on essential protein–protein interaction prediction by integrated edge weights. Methods 83:51–62.Crossref, Google Scholar
- (2005) High-betweenness proteins in the yeast protein interaction network. BioMed Res. Internat. 2005(2):96–103.Google Scholar
- . (2003) Systematic functional analysis of the Caenorhabditis elegans genome using RNAi. Nature 421(6920):231–237.Crossref, Google Scholar
- (2004) Bioinformatical assay of human gene morbidity. Nucleic Acids Res. 32(5):1731–1737.Crossref, Google Scholar
- (2000) Genome-wide protein interaction maps using two-hybrid systems. FEBS Lett. 480(1):32–36.Crossref, Google Scholar
- (2010a) On network-based kernel methods for protein-protein interactions with applications in protein functions prediction. J. Systems Sci. Complexity 23(5):917–930.Crossref, Google Scholar
- (2010b) Essential proteins discovery from weighted protein interaction networks. Borodovsky M, Gogarten JP, Przytycka TM, Rajasekaran S, eds. Bioinformatics and Applications, ISBRA 2010, Lecture Notes in Computer Science, vol. 6053 (Springer, Berlin), 89–100.Google Scholar
- (2014) Effective identification of essential proteins based on priori knowledge, network topology and gene expressions. Methods 67(3):325–333.Crossref, Google Scholar
- (2010c) Computational approaches for detecting protein complexes from protein interaction networks: A survey. BMC Genomics 11(Suppl 1):S3.Crossref, Google Scholar
- (2013) DEG 10, an update of the database of essential genes that includes both protein-coding genes and noncoding genomic elements. Nucleic Acids Res. 42(Database issue):D574–D580.Google Scholar
- (2010) Features analysis for identification of date and party hubs in protein interaction network of Saccharomyces cerevisiae. BMC Systems Biol. 4(1):172.Crossref, Google Scholar
- (2013) Integrative approaches for finding modular structure in biological networks. Nature Rev. Genetics 14(10):719–732.Crossref, Google Scholar
- (2011) Modularity detection in protein-protein interaction networks. BMC Res. Notes 4(1):569.Crossref, Google Scholar
- . (2005) The MIPS mammalian protein–protein interaction database. Bioinformatics 21(6):832–834.Crossref, Google Scholar
- (2017) Protein–protein interactions: Detection, reliability assessment and applications. Briefings Bioinform. 18(5):798–819.Google Scholar
- (2004) Detection of functional modules from protein interaction networks. Proteins 54(1):49–57.Crossref, Google Scholar
- (2011) Prediction of essential proteins by integration of PPI network topology and protein complexes information. Bioinformatics Research and Applications (Springer, Berlin), 12–24.Crossref, Google Scholar
- (2004) The database of interacting proteins: 2004 update. Nucleic Acids Res. 32(Suppl 1):D449–D451.Crossref, Google Scholar
- (2011) Building protein-protein interaction networks with proteomics and informatics tools. J. Biol. Chemistry 286(27):23645–23651.Crossref, Google Scholar
- . (2011) A conditional knockout resource for the genome-wide study of mouse gene function. Nature 474(7351):337–342.Crossref, Google Scholar
- (2003) How reliable are experimental protein–protein interaction data? J. Molecular Biol. 327(5):919–923.Crossref, Google Scholar
- . (2014) STRING v10: Protein–protein interaction networks, integrated over the tree of life. Nucleic Acids Res. 43(Database issue):D447–D452.Google Scholar
- (2014) Predicting essential proteins based on weighted degree centrality. IEEE/ACM Trans. Comput. Biol. Bioinform. 11(2):407–418.Crossref, Google Scholar
- (2014) Network inference from AP-MS data: Computational challenges and solutions. Briefings Bioinform. 16(4):658–674.Crossref, Google Scholar
- (2015) Bacterial protein networks: Properties and functions. Nature Rev. Microbiol. 13(9):559–572.Crossref, Google Scholar
- (2015) An integer programming approach for finding the most and the least central cliques. Optim. Lett. 9(4):615–633.Crossref, Google Scholar
- (1977) Biochemical evolution. Annual Rev. Biochemistry 46(1):573–639.Crossref, Google Scholar
- (2003) Centers of complex networks. J. Theoret. Biol. 223(1):45–53.Crossref, Google Scholar
- (2000) DIP: The database of interacting proteins. Nucleic Acids Res. 28(1):289–291.Crossref, Google Scholar
- (2004) Genomic analysis of essentiality within protein networks. TRENDS Genetics 20(6):227–231.Crossref, Google Scholar
- (2007) The importance of bottlenecks in protein networks: Correlation with gene essentiality and expression dynamics. PLoS Comput. Biol. 3(4):e59.Crossref, Google Scholar
- (2002) MINT: A molecular interaction database. FEBS Lett. 513(1):135–140.Crossref, Google Scholar
- (2009) DEG 5.0, a database of essential genes in both prokaryotes and eukaryotes. Nucleic Acids Res. 37(suppl 1):D455–D458.Crossref, Google Scholar
- (2004) DEG: A database of essential genes. Nucleic Acids Res. 32(suppl 1):D271–D272.Crossref, Google Scholar
- (2008) Why do hubs in the yeast protein interaction network tend to be essential: Reexamining the connection between the network topology and essentiality. PLoS Comput. Biol. 4(8):e1000140.Crossref, Google Scholar

